


The Enemy Within

by kez



Category: Stargate Atlantis
Genre: Angst, Child Death, Established Relationship, M/M, Mpreg, Original Character Death(s), Violence
Language: English
Status: Completed
Published: 2012-01-30
Updated: 2012-01-30
Packaged: 2017-10-30 08:42:31
Rating: Mature
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 14,074
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/329912
Author URL: https://archiveofourown.org/users/kez/pseuds/kez
Summary: <blockquote class="userstuff">
              <p>An encounter with the Wraith has consequences for John Sheppard that no-one could have forseen.</p>
            </blockquote>





	The Enemy Within

**Author's Note:**

  * For [scap3goat](https://archiveofourown.org/gifts?recipient=scap3goat).



> This was written a long time ago, for scap3goat as part of the Beckett Request-a-thon, the prompts were mpreg and darkness, which don't typically go together in my mind, but hopefully I've done it justice. Many thanks to Morri for the killer idea of... well I can't say what, because that would give away the plot and to Laura for the beta.
> 
>  
> 
> **This story does contain a fairly dark subject matter and the resolution may upset some readers - for more specific spoilers please see end notes.**

Day 1: Early Morning: P3X-779

"McKay, get down!" Sheppard yelled, practically rugby tackling the scientist to the ground, less than a split second ahead of the blast from the Wraith stunner that was being directed at them.

Sheppard counted the Wraith as best he could in his head, nine against four, so not a fair ratio. "Teyla, Ronon, you guys okay?" he asked quickly over his radio, they were on the other side of the ruins they'd been exploring; the Wraith had come in so fast they had no chance to prepare.

"We are fine Colonel, the Wraith do not seem concerned with us, they appear to be concentrating most of their fire towards you and Doctor McKay." Teyla's voice came back through his headset.

"Great. Get behind them, we'll keep them distracted." Sheppard told her, quickly rolling up, firing off several shots before ducking again.

"Are you crazy?" McKay looked incredulous. "Oh God, we're going to die."

"Not today McKay, I have plans." Sheppard said, shooting off several more rounds of fire, the Wraith were converging on their position.

"Move!" Sheppard hissed, pushing McKay further into the ruins, maybe they'd get lucky and the ruins would fall down on the heads of the Wraith. Of course, it was far more likely they'd be crushed, but at least then the Wraith wouldn't be able to snack on them. Somehow, Sheppard didn't think the Wraith menu extended to Human pancakes.

"Colonel, we're approaching your position," Teyla's voice fizzled in his ear, something was affecting the reception, but as long as he could still hear her, he wasn't that concerned. "A Wraith dart has just come through the gate." Teyla informed him quickly. Sheppard cursed inwardly, this was not his day, didn't these people realize he had plans for tonight, plans that while involving a certain member of the medical profession did most definitely not involve the infirmary.

Sheppard felt the sting of something hitting his arm. It just figures I had to wear a t-shirt today! Sheppard thought irritably, before he blacked out to the sound of McKay shouting his name.

~~~~~

Day 1: Mid-Morning: Atlantis: Gate Room

Teyla and Ronon dragged an unconscious McKay through the gate with them; he'd been hit by a Wraith stunner, but left alone and alive.

Beckett quickly attended to him, ordering his team to take him to the infirmary, he knew well it would be sometime before McKay woke up and until then there was little they could do except keep him comfortable.

"Where is Colonel Sheppard?" he asked, once McKay was safely on his way to the infirmary, Beckett had looked around for him and realized, he wasn't there.

"He was taken by the Wraith." Ronon answered, tact was not his strong suit and evidently he was irritated that the Wraith had attacked them and made off with Sheppard, clearly this didn't make him anymore inclined to be tactful. 

Beckett paled. "The Wraith were behaving most unusually. They took the Colonel but did not kill McKay despite the fact he was with the Colonel when he was taken, they made no move to kill us either, almost from the moment they arrived on the planet, they seemed interested only in Colonel Sheppard." Teyla explained.

"Why?" Beckett asked the obvious question. Obviously, the one Teyla did not have the answer too.

"Carson, why don't you go see how Rodney is doing? Major Lorne, get your team together and meet me in the briefing room." Weir instructed.

Beckett nodded numbly, he wanted to argue, to shout and yell, but he knew his position was precarious, everyone on Atlantis knew about his relationship with Sheppard, but no one mentioned it. Don't ask, don't tell.

Turning to walk towards the infirmary, he paused when Teyla touched his shoulder. "If it is of any comfort, I do not believe the Colonel is dead, I do not know their reason for taking him, but to take him and leave us unharmed is unfounded behavior for the Wraith, they must have a reason beyond simply killing him."

"Aye, thanks," Beckett said, though he wasn't sure if that did comfort him or not, if the Wraith didn't simply want to kill Sheppard, then he didn't want to imagine what they were doing to him, but Teyla was only trying to help.

~~~~~

Day 1: Mid-Morning: Atlantis: Briefing Room

Weir sat across the table from Teyla, directing most of her questions towards the Athosian woman.

"The only time I know of where a Wraith has taken a single individual is Runners, however on those occasions they always killed all others near by; I do not understand their reasoning in allowing us to live." Teyla said. Her face was calm, but her voice gave away her concern. She was confused by the Wraiths behavior, she had never seen them act in such a manner, it was most disconcerting.

"Do we know where they took him?" Lorne asked.

Teyla shook her head negatively. "The Wraith used the DHD on their dart. We had no way of seeing the symbols; however, I saw the last two as they were locked on the Stargate."

"There are still thousands of possible permutations," Zelenka said, then pausing to think a moment added, "however, maybe the ancient database will be able to narrow it down."

"Do it, Major, prepare your team for search and rescue and order Bates and Stackhouse to put together teams as well." Weir added.

Lorne nodded shortly and left with his team, leaving only Weir, Teyla, Ronon and Zelenka.

"Ronon, can you think of any other reason, aside from as a Runner, the Wraith might want Colonel Sheppard?" Weir asked.

"No. And I do not believe they want him as a Runner. The Colonel is skilled in combat; however he would likely not survive continued hand to hand combat with the Wraith." Ronon said. It wasn't an insult, or at least he didn't intend it to be.

"Perhaps," Teyla started, pausing for a few seconds before she continued, "it has something to do with the ancient gene the Colonel possesses. It is possible the Wraith have come to the same conclusion Doctor Beckett did and wish to attempt a therapy on themselves such as was given to Doctor McKay."

Teyla could see the concern in Weir's face when she considered that. It was indeed a most unpleasant idea, because not only could it give the Wraith the ability to use ancient technology, but also, because of what it suggested they might be doing to Sheppard in their efforts to effect the gene therapy.

~~~~~

Day 4: Wraith Planet

Sheppard groaned and rolled onto his side, his whole body was sore. His first attempt to open his eyes had him closing them again quickly; the room was almost entirely dark except for one glaringly bright white light shining directly on him.

He felt around himself, slowly opening his eyes trying to adjust to the light. Where am I? He thought, biting his lip to prevent a scream as he fell over the edge of the bench like stone platform he'd been lying on. Desperately he tried to think where he was, where he'd been, what was happening.

The last thing he remembered was being on P3X-779, the Wraith were coming after him and McKay... McKay, Teyla, Ronon... where were they? Were they here, or had they gotten away, or... he refused to complete the final thought. He heard footsteps and tried to get up, but his body felt like it was made of lead. Lead being poked with millions of tiny pins, but lead nonetheless.

"Ah. Awake again. Good." Sheppard looked up to see who was talking and very quickly realized where he was, when he came face to face with a Wraith.

"Bring him!" the Wraith ordered as two others came out of the shadows and lifted him bodily.

"Let me go!" Sheppard tried to struggle, but it was pointless, he wasn't going anywhere. The last thing he knew for quite a while was the sting of some sort of needle in his arm and a dull pain in his abdomen.

~~~~~

Day 12: Evening: Atlantis: Briefing Room

Major Lorne's team had just come back from yet another trip through the gate. The Atlantis database, with McKay's steering, had narrowed down the possibilities from several thousand to one-hundred-eighty-seven, but that still left too many planets for them to explore. It would take months, even with four teams going out almost daily.

"Major, anything?" Weir asked, but she already knew the answer, if they'd found any sign of Sheppard they'd have reported in for reinforcements, or rescued him themselves... assuming... Weir sighed mentally, she wasn't ready to go down that road, but it seemed there was no other choice.

"No ma'am, there were signs the Wraith had been there, but no recent activity," Lorne reported apologetically.  
"Thank you Major, dismissed." Weir told him, watching him leave so she could avoid looking at the others still seated. Sheppard's team, along with Beckett, Zelenka and Bates were all waiting for her to speak.

Weir looked at Beckett when she finally looked back towards the gathered people. She was sure he knew what she was about to say before she even said it. "Colonel Sheppard will be listed MIA, we'll keep looking while carrying out our regular off-world missions but..." she didn't need to finish the thought and though she hadn't said it, they could all hear the unspoken 'presumed dead'.

She watched Beckett pale, could see the tears forming in his eyes and was sure that later, when they were all alone, Beckett wouldn't be the only one shedding a tear for Sheppard, wherever he was.

"Dismissed." She added her voice gravelly as she tried to keep her own emotions locked up until she was alone.  
"Elizabeth..." Beckett stayed behind after the others had gone.

"Carson, I'm sorry, I really am, but however much I might want to I can indefinitely suspend normal operations." Weir said, her face and voice were apologetic and she knew he didn't blame her, but knowing how Beckett felt about Sheppard, it was hard to face him now.

"I know. Could I have a few days to... I could go to the mainland and..." Beckett paused, clearly hurting, his accent thickening.

"Of course you can, either here or on the mainland I'll make sure you aren't disturbed unless it's an emergency." Weir assured him. She stood up and gave him a hug, watching him go before she let herself drop back into her seat, tears in her own eyes.

~~~~~

Day 13: Morning: Mainland

Beckett woke slowly, light was streaming in the windows of the Puddle Jumper, he was groggy from too little sleep, or maybe it was too much he thought, he had no idea what time it was. He'd visited the Athosians yesterday just long enough that Weir wouldn't be concerned and to pick up some of their local brew. Strong enough to knock out an ox, it wasn't something Beckett normally indulged in, but last night he'd made the exception.

He was paying for it now, his head felt like a brass band was practicing inside and the drummer was using the back of his eyeballs in place of a drum. The worst thing about it was that despite his best intentions; it didn't prevent him from thinking.

He remembered the first time he'd meet Sheppard, in Antarctica, he'd practically killed the man and he'd just given a lop-sided smirk and told him to be more careful next time. Of course, Sheppard had known nothing about the Stargate or the Ancients.

Then they'd come to Atlantis, with all its wonders and its dangers, but they never could have imagined the Wraith. Beckett had never come face to face with a Goa'uld, but he imagined he'd sooner face them than the Wraith; at least the Goa'uld didn't snack on people... not that he knew of anyway, though he did seem to remember something in one of Daniel Jackson's reports about them eating other Goa'uld symbiotes.

Sheppard was constantly in and out of the infirmary and after he'd been bitten by the Iratus Bug, they'd become friends, so to speak, they'd spent a lot of time talking and had found, surprisingly, they had several things in common. Although, Beckett had still insisted, much to Sheppard's amusement, that anyone who enjoyed flying was crazy.

It had taken time, but after Sheppard had 'died' during the Wraith Siege of the city, those few moments when Beckett had been in the control room and they'd all believed he was dead, Beckett had realized the attraction he'd felt to Sheppard was more than just a crush, he was in love. Somehow Sheppard had felt the same and even while they dealt with putting things back together after the siege Beckett had felt like he was on cloud nine.

Things were never easy, but they'd made it work through all the everyday craziness on Atlantis and now... Beckett choked up, feeling the pain welling inside him, it was too much, Sheppard was... gone.

~~~~~

Day 19: Morning: Unknown Planet

Sunlight was just starting to peek over the horizon when Sheppard opened his eyes. His memory was vague, but he knew wherever he was, he was no longer with the Wraith, nor was he on Atlantis.

"Oh, you’re awake, we were afraid you weren't going to wake up." The young girl who spoke startled Sheppard. She wasn't much more than fifteen he thought, wearing very simple clothing, with curly brown hair tied back.

"Where I am?" Sheppard asked, coughing, when was the last time he'd had water?

"Rurelin. Here, drink this." The girl answered, handing him a cup. An experimental sniff suggested it was water and he drank it gratefully. "You were found three days ago by one of our hunting parties in the woods. All the things that were with you are over there on the bench, we didn't touch anything."

Sheppard glanced over and sure enough, his kit appeared to all be there. When he got up to check it he felt the stinging pain in his side.

"You were injured, whoever stitched your wound did a poor job, our healer had to do it again." The girl, who Sheppard realized, he still had no name for explained when he looked at the angry red mark across the left side of his abdomen.  
"Thanks. What's your name?" Sheppard asked her.

"Fren Kallik, but you can call me Fren. The name... Sheppard... is that correct? Was on your clothing." Fren said, speaking slowly when she said his name.

"Yeah. John Sheppard. John is fine." He said as he checked through all his equipment. Everything seemed to be there and still working.

"Fren, listen do you guys have a Stargate, a big ring with lots of symbols?" Sheppard asked.

"The Gladin, yes, it stands in a field two days walk from here." Fren told him.

"Two days... I don't suppose there is a faster way to get there?" he asked, already concerned wondering how long he'd been gone.

"Of course, we have a cart and our Juke are fast, they can travel the distance in less than a day." Fren said.

"Well, I need to get there, so I can get back to my people, if you could take me..." Sheppard tried to think what he could offer in return, but there wasn't a lot in his kit that was good for trading.

"I will take you, after you have eaten, you haven't had food in at least three days and you will need your strength." Fren insisted. As if her words reminded him of food, his stomach started to grumble.

"I could eat." Sheppard agreed.

~~~~~

Day 19: Evening: Atlantis: Gate Room

Weir was leaning against the rails of the control room facing Zelenka. "Radek, how are we doing on..."

"Unauthorized off-world gate activation." The gate tech said, as the Stargate came to life beneath them. "We're receiving an IDC..." The techs eyes went wide as he looked at Weir. "It's Colonel Sheppard's."

Weir and Zelenka both looked at him, as if asking for confirmation. He nodded; the IDC they were receiving was definitely John Sheppard's.

"Security teams to the gate room. Lower the shield and green light him." Weir ordered after a few moments paused consideration.

Weir made her way down the stairs quickly, Zelenka trotting along behind her as the security teams got into place guns aimed at the gate. Everyone was watching the Stargate, it seemed like if a pin dropped three floors down, they'd hear it like a resounding clatter in the silence.

A few moments later the disheveled form of John Sheppard walked through the gate. He had a short beard but both he and his clothing looked clean.

"What no party balloons?" he asked casually.

Weir looked at him, really looked at him, like she could physically see his insides, she was looking for anything out of place, a person did not just disappear for nearly three weeks and just walk back through the Stargate like he'd been out for an afternoon stroll.

"Or not. Elizabeth, why are there guns pointed at me?" Sheppard questioned cautiously.

"Sergeant Bates, disarm the Colonel." Weir instructed.

"Hey now just hang on a moment!" Sheppard protested as he was disarmed and patted down. "Oh I'm making sure Carson gives you the biggest needle he has next time you're in the infirmary."

Sheppard's comment reminded her of Beckett. He'd been so careful to keep up his professional façade since he'd returned from the mainland a couple of days before, but it was clear that the time since Sheppard had gone missing, especially the five days since she'd listed him MIA had affected the Doctor greatly. 

If this wasn't really Sheppard... he looked like Sheppard however, sounded like him, but if it was some Wraith trick... "Sergeant, escort the Colonel to the briefing room," Weir ordered. She could tell Sheppard was confused and a little miffed when he cursed quietly.

"Exactly how long was I gone?" Sheppard asked as Bates carted him off to the briefing room.

"Radek, keep an eye on him, I want Carson to check him out but I think I'd better warn him first." Weir instructed the scientist. "And have Sheppard's team sent down to the Infirmary as well." She added.

~~~~~

Day 19: Evening: Atlantis: Infirmary

"Well who else could it be?" Beckett asked. Really he understood Weir's concern but surely the Wraith didn't have the ability to clone humans otherwise why would they need to hunt for food when they could make their own?

"Carson, I know... When he came though the gate, I want to believe it's really John, but we need to take precautions. If you can't do it no one will think any less of you, one of the others can do the tests and..."

"No! I can do them." Beckett insisted. Weir nodded and he mentally began trying to prepare himself. He thought he had himself under control until the moment Sheppard walked in the door flagged by Bates and Zelenka.

Eyes he knew so well looked at him, begging recognition and for a moment all Beckett wanted to do was fall into the arms of his lover, but Weir was right, they had to be cautious, no one really knew what level of technology the Wraith had, certainly they had their own advanced sciences, anything was possible.

"Jump up," Beckett said patting the bed, he turned around to gather both his instruments and his thoughts, pushing anything that wasn't medical to the back of his mind before turning back to begin his tests. He tried to ignore the look of distress on Sheppard's face.

Sheppard was really trying to understand Weir's concern, from what she's said, he'd been missing for the better part of three weeks and to have him suddenly turn up almost entirely unharmed except for the nicely healing wound on his abdomen had to be weird, but he couldn't help feeling a little hurt, especially by Beckett's reaction.

He'd been so sure when Beckett saw him he'd know it was him right away, without needing any stupid tests, but the Doctor was almost icy towards him.

Weir kept throwing questions at him, at first about his time in captivity with the Wraith, then to more personal subjects, trying to catch him out on a lie, if he was an imposter.

"Look, I get the caution, but I'm me! John Sheppard, Lt Colonel in the USAF, thirty-six years old, born November fourteenth, nineteen-seventy-four. My parents are Alexander and Kathryn Sheppard; I'm an only child..." Sheppard caught himself on that one, Weir of course had read his file, but no one else here, not even Beckett knew about...  
"I'm me damn it!" Sheppard added, including a healthy dose of irritation in his tone.

"Colonel, please, just let Doctor Beckett finish his tests." Weir asked.

Sheppard sighed tiredly. He just wanted to be left alone, to go back to his quarters and fall into bed until oblivion over took him. He was tired and hurting, emotionally more than physically, he just wanted to sleep and wake up to realize this was all a horrible dream.

"I'll get these done right away." Beckett said, putting a band-aid over the place he'd taken blood and quickly abandoning his patient.

~~~~~

Day 20: Afternoon: Atlantis: Infirmary

"Well it’s definitely him," McKay said, "only Sheppard could be this irritating"

"Well thanks, McKay. That was almost a compliment coming from you." Sheppard growled.

McKay shrugged, he could understand Sheppard's irritability, I mean he'd be irritable if the Wraith had kidnapped him for three weeks. Even more so since everyone was being 'cautious' and no one was actually being all that welcoming incase it was some Wraith plot.

"I am still unsure why the Wraith would just let you go." Teyla said. McKay rolled his eyes, they'd been over this several times, it was pointless really and getting old.

"And we may never know, lets just be grateful they did," McKay said. Which was getting dangerously close to complimentary, but McKay had to admit, if only to himself, he cared about Sheppard, not like that, he'd leave that to Beckett, but Sheppard was his friend, probably one of the few real friends he'd ever had and that meant a lot to him.

"Look here comes Carson to agree with me... right? The DNA tests conclude its him?" McKay asked, entirely ready to be correct.

"Aye, DNA tests are conclusive, there isn't even a slight differential in his DNA, he's not a clone." Beckett agreed. "But the other tests..."

~~~~~

"What about the other tests, Doctor?" Weir asked him. Beckett looked at her, was there any acceptable way to say this? Probably not, he'd had six hours of tests and retests to try and figure out a way of saying it and there just wasn't one.

"Colonel Sheppard's blood shows a measurable amount of the hCG hormone normally found in women who are... pregnant." Beckett said, vainly keeping his professional face in place.

""What!?!" Sheppard exploded and for a moment Beckett thought to step back, but he held his feet, he had to be professional here, he couldn't let his personal feelings get in the way, not when he'd spent all of last night working so hard to reign them in and keep them in.

"I ran the tests several times, they're conclusive. I'd like to do some X-rays of the area where you were wounded." Beckett said, keeping his eyes firmly locked on Sheppard's, desperately hoping he was keeping his composure as well as he was trying to.

~~~~~

Sheppard slumped backwards onto the bed. This was all some horrible nightmare. Beckett looked at him with cool detachment, as if they hadn't woken up wrapped around each other a dozen times in recent memory. He was standing there telling him he was displaying signs of a hormone he shouldn't physically be capable of making, a hormone that suggested he was pregnant and he wasn't showing a single sign of caring about Sheppard more than he would anyone else he'd ever treated.

This wasn't even amusing anymore. All morning he'd been bantering with McKay answering stupid questions and throwing insults back and forward with the scientist. It had been amusing if slightly irritating and he'd finally started to rationalise Beckett's behavior sure it would revert to the norm once the DNA tests were in, but clearly that wasn’t going to happen.

~~~~~

Day 20: Evening: Atlantis: Infirmary

"These are the scans I took, you can clearly see here..." Beckett pointed at the x-ray on the wall, "this is some sort of artificial womb."

Weir looked at Sheppard who was sitting staring blankly at the x-ray. "Is there anything we can do to remove it?" she asked, concern etched on her face.

Beckett shook his head, "I wouldn't like to chance it, it's in a very delicate place, how they were even able to do this I don't know, without knowing more about the process, I'm not convinced it's worth the risk."

Weir nodded understandingly, but she was still watching Sheppard, he looked lost.

"John..." she murmured moving closer to him, placing a reassuring hand on his arm. Green eyes looked up at her, Sheppard was military, but any training he'd had went right out the window then, he was petrified and Weir could see it as plain as daylight.

"We'll figure it out," she promised him quietly, hoping beyond hope she wasn't lying.

~~~~~

Day 21: Morning: Atlantis: Infirmary

"He's asleep, I gave him a mild sedative." Sheppard heard Beckett's voice, it was soft, muffled almost, but there was no mistaking it for his. He opened his eyes slowly but closed them again, light was highly overrated he decided. 

Sheppard kept his eyes closed but strained his ears to hear who Beckett was talking to, it only took a moment for him to place the voice as belonging to Weir. "How about you? Have you slept?" 

"A little, I don't want to leave him alone. I know I'm supposed to be keeping things professional, and I am, but..."

Weir interrupted him. "Carson, no one cares about you two. It's not exactly a secret. I think he needs *you* more than his Doctor right now."

"Aye, maybe, but what am I suppose to say to him? It's like with that damn retrovirus, I couldn't hardly look at him during that, keeping things professional was the only way I could handle it. It would just be like me to fall for someone like him, would be a lot easier if I hadn't." Beckett said.

Sheppard stopped breathing for a moment, frozen... was Beckett saying he didn't want to be with him anymore?

"You don't mean that, you're scared, you have the right to be." Weir told Beckett gently.

"No, I don't. John has the right to be, not that he'll admit it out loud mind, he's more stubborn than a mule. But aye, you're right I don't mean it. I love John, more than anything, that's why this has me so turned about, I want to just hold on to him and never let go, but I *need* to work on finding a way to fix this."

Sheppard continued to listen to Beckett and Weir discussing him quietly for another few minutes, until he realized he no longer heard their voices, only the sound of quite foot treads, Weir's he guessed, moving away. 

He must have dozed off, he realized, when he felt the soft sting of a needle in his arm.

"Carson?" he asked sleepily.

"Aye, its me. I'm just giving you something for pain, you go back to sleep." Beckett told him softly.

Sheppard shook his head, trying to shake away the cobwebs of sleep. "I'm not tired, just... I missed you."

~~~~~

Day 21: Afternoon: Atlantis: Infirmary

Beckett watched as Sheppard slipped back into sleep, his eyes softening as Sheppard mumbled 'I missed you'. He'd missed Sheppard too. Beckett was going to go and run further tests, but instead he pulled a chair over beside Sheppard's bed and sat down, carefully taking Sheppard's hand in his.

Apparently Sheppard wasn't the only tired one, because the next thing Beckett was aware of was the feeling of a hand running through his hair. He turned his head and realized he'd leaned forward, his head rested beside Sheppard's hip, and fallen asleep.

Sheppard looked back at him with eyes both hopeful and sad. "How are you feeling?" Beckett asked softly, leaning into the gentle fingers massaging his scalp.

"Okay. I think, I'm... not really sure." Sheppard admitted quietly.

"Understandable." Beckett told him, sitting up and taking Sheppard's hand in his again, bringing it up to place a kiss on the side of his wrist. "We'll figure it out."

Sheppard didn't look convinced, but seemed happy just to hear it.

"I missed our date." Sheppard said, changing the subject.

"You had a really good excuse, so I'll let you off this time, just don't do it again." Beckett told him, smiling and trying to hold back the tears. He was so sure he'd never see Sheppard again, this was like a second chance and for a few minutes they were able to just pretend that things were normal, until Sheppard complained of feeling queasy and emptied his stomach contents into a bedpan.

"Easy, love," Beckett murmured softly, rubbing Sheppard's back. Morning sickness or maybe it was mid-afternoon sickness, either way Sheppard had paled considerably and was barely able to do more than sit and dry-heave for minutes after the sickness passed.

"Carson..." Sheppard mumbled as Beckett helped him lay back.

"It's okay, love, I'm not going anywhere." Beckett promised. He wouldn't let Sheppard go through this alone, he'd find some way to fix it and if he couldn't he'd be there every step of the way to help Sheppard deal with it.

~~~~~

Day 27: Afternoon: Atlantis: Sheppard's Quarters

Sheppard was bored, bored and more bored. He'd cleaned up... not that there was much to tidy,; years in the military, not to mention growing up in a military home, had trained him to keep his room clean. He'd read a whole chapter of War and Peace... and been mind numbingly bored when doing so. He had even been reduced to playing solitaire on his laptop.

Beckett was working, his team was off-world, Weir was busy doing whatever it was she did in her office... paperwork probably. Sheppard was actually so bored he thought about offering to help her with the paperwork, he'd even thought about going to Zelenka and offering to touch things in the lab just to give him something to do.

He'd been relieved of duty until further notice. Weir had the good grace to look suitably sorry for doing so, but Beckett had helpfully pointed out that his 'condition' as he referred to it probably wouldn't last more than five or six months at its current rate of progression... yah like *that* made him feel better.

He didn't want it to progress, he wanted the damn thing out of him and no matter how much Sheppard argued his point, Beckett - and Weir, the traitor - refused to attempt surgical removal.

"It's too risky." Beckett had told him, risky compared to what exactly, Sheppard wondered. Surely the Wraith didn't do this just for kicks, didn't any of them realize there could well be a ticking time bomb inside him?

The only saving grace... if it could even be called that, was that Weir was still letting him fly between Atlantis and the mainland, so long as he never went out alone and always checked in with Beckett on his return.

Still, it was almost too much trouble so he'd only flown out to the mainland twice. Beckett was working constantly to try and figure out some way to help him, but it meant he saw very little of him. Sheppard was grateful for Beckett's work towards helping him, but irritable because it meant he spent all day and some nights, almost entirely alone.

On top of everything, he was already noticing changes in his appearance, not yet noticeable when he was dressed, but it wouldn't be long. Sheppard felt sorry for every woman he'd ever known who'd gone through this, but at least, he reasoned to himself, their bodies were designed for it, oh and they weren't carrying a Wraith!

Eventually, Sheppard gave in, pulling on his trousers and one of his loosest t-shirts, he headed for the science labs to find Zelenka, at least it would give him something, anything, to do but stare at the four walls of his room.

~~~~~

Day 34: Evening: Infirmary

"Ouch, hey, take it easy!" McKay complained loudly, pulling his arm away from Beckett.

"Sorry," Beckett replied on cue, still sounding perfectly surly.

"Yes I can see that, oh no, you keep your needles to yourself, one huge bruise is enough for one day, people will start thinking I'm a battered husband." McKay insisted pulling away from the irate Doctor.

Beckett rolled his eyes at McKay's exaggerated response, to a tiny needle. Okay maybe, Beckett would concede, he'd been a little rougher than he would normally be, but it was hardly that bad.

"How is Colonel Sheppard?" McKay asked. Beckett glanced at him; it wasn't fair that a man with the social finesse of a wild chicken, could so easily read through all the BS and right to the heart of a problem.

"He's fine." Beckett answered quickly. To quickly he knew, because McKay gave him a look that said 'pull the other one, its got bells on it', or at least it might have said that, if McKay would ever lower himself to that standard, but still, the look was clear, McKay didn't believe him.

"Irritable. He is still getting 'morning sickness', mostly in the evening and he's starting to show a wee bit." Beckett said instead.

"That tells me how he is physically," McKay conceded, waiting for more.

"I don't know, okay, he won't talk to me, 'cept maybe to shout at me because I can't fix this. He's frustrated, but he just won't talk to me." Beckett admitted, feeling better about telling someone at last. Sheppard had only been back in the city two weeks, but they were some of the longest weeks of Beckett's life. At first, after Sheppard had come back, Beckett had tried to keep things professional; when he had eventually cracked... it had been so good to let Sheppard hold him again, but after those first few days, Sheppard got crankier. He wouldn't tell Beckett what was on his mind, wouldn't let him share the burden and no matter how much Beckett was sure it wasn't his intention, Sheppard screamed 'I blame you' every time he looked at Beckett.

"Military stubbornness," McKay said like that explained it all perfectly. "I could talk to him." Beckett snorted, McKay was a good friend, but tact wasn't his strongest suit.

"Thank you, Rodney, but I think we just need to deal with it ourselves, still, I'm sure he'd like to see a friendly face for a while, you could keep him entertained." Beckett suggested.

"Hmm... well if I have time, maybe after lunch, which is now. Are you going to try jabbing me to death again or can I go?" McKay asked.

Beckett smiled softly, McKay, for all his social ineptitudes really was a good friend. "Go, eat and stay away from brambles next time." Beckett warned.

Maybe he should have taken McKay's officer, maybe Sheppard would open up more to him, but why the heck would he, why couldn't he open up to Beckett, they were suppose to be there for each other, but as quickly as he thought things had been fixed with them things had fallen apart, he just had no idea what to do.

~~~~~

Day 45: Morning: Balcony: Sheppard's Quarters

Sheppard had barely been outside in three days, except for meals and to visit the infirmary, not since he'd realized his trousers were too tight and since they were already a size too big then he had to have put on weight, which could probably be seen by everyone. Beckett had tried to reassure him he looked fine, but it had only ended in an argument, like most of their conversations did lately.

In all honesty, Sheppard knew he was being unreasonable, he really didn't mean to be, but his moods were all over the place and Beckett got so... doctor-ish... like he didn't know it was just hormones, he may not have planned for this situation but he'd been there through three of his mothers pregnancies, he knew the drill.

He wondered how his mother had coped with it, especially after the third miscarriage, she had been so close to the due date that time they'd already had her hospital bag packed. But then his grandma had woken him in the middle of the night, 'get dressed Johnny', she'd told him, by sun-up he'd been once again confirmed an only child.

Sheppard winced when he felt the flutter of movement in his abdomen. It wasn't painful, but he was totally unprepared for it. It felt like... like what he thought water sloshing around a jar might feel like, except for sharp little jabs that he could only assume were kicks, as he had no comparison.

Wriggling uncomfortably or mentally ordering the movement to cease didn't seem to be working, the... Sheppard still wasn't sure what he should call it, somehow the words baby and wraith didn't mesh well in his head, but that’s what everyone else called it... the baby seemed as restless and uncomfortable as Sheppard himself was.

Putting a hand to his stomach where the slight bump showed, Sheppard rubbed soothing circles there. He'd seen his mother do it when she was pregnant and it seemed normal to do it now, if, Sheppard reflected wryly - right before another kick centered on his gut - anything about this situation could be called 'normal'.

It seemed, however, to work; after a few minutes the movement lulled to a stop but instead of stopping, Sheppard leaned back against the wall, watching the ocean and continued his movements, trying to keep his mind clear. It seemed logical really, he reasoned, the Wraith were telepathic, with each other at least, to a certain extent, there was no reason to assume this baby, being at least half wraith, wasn't also.

~~~~~

Day 45: Afternoon: Infirmary: Beckett's Office

Beckett was hiding. Not that anyone was probably trying to find him; least of all the person he was actually hiding from, Sheppard was determined not to leave his quarters. Still, Beckett hid; it seemed the thing to do, after all, when one didn't want to be found. 

He probably wasn't even very well hidden, anyone who really wanted to find him would probably find his office a smart place to look, but he was fairly convinced no one was looking for him, so he wasn't that bothered.

He'd spent all morning working on samples he had of Wraith DNA, the retrovirus was, he was confident, coming on in leaps and bounds. Though they wouldn't know for sure for a long time to come, Beckett had no intention of testing it on a living thing again in the near future.

Eventually, at lunch, he'd decided to go and see if Sheppard was hungry, truthfully he was hoping Sheppard would be in a better mood than he had been that morning and sure enough Sheppard looked calmer when Beckett had arrived, which was good until he realized *why* Sheppard looked calmer.

He was on the balcony, hadn't even heard Beckett enter. He was leaning against the wall casually, one hand by his side while the other rubbed soothing circles on his stomach. It worried Beckett. He was worried what this pregnancy could do to his lover, both physically and emotionally. 

So far it seemed most of the symptoms had indeed been emotional and all the emotions seemed to be negative, anger, hurt, frustration, generally directed at Beckett himself, but he could handle that, or he could try to. Things were very up and down and Sheppard wouldn't talk to him about how he was feeling unless it was to yell at him, but at least while Sheppard was yelling he had some idea what he was feeling. How was he supposed to read the situation now?

Was Sheppard becoming attached to the baby? What could that mean exactly? For Sheppard himself, for their relationship, for all of Atlantis?

~~~~~

Day 50: Night: Briefing Room

"He's becoming attached to the wraith baby and more withdrawn from everyone else." Beckett said.

Weir nodded, she understood Beckett's fears, she'd considered this very thing herself, that Sheppard would become attached to the child. What would happen, if he decided he wanted to keep it? Was there a chance the retrovirus would work? Could Sheppard's child be 'normal'? If so, Weir didn't see how she could stop him keeping it, although, he would most certainly be sent back to Earth. If not, Weir didn't imagine how she would be able to take the baby from him without completely destroying their relationship and probably forcing Sheppard to return to Earth, because he wouldn't want to be around the people who'd taken his child.

It was all theoretical really; there was every chance in the world Sheppard would want to be rid of the baby as soon as possible. Certainly, the few times she had seen him, before he went into hiding, he was adamant he wanted it gone, in fact they'd argued quite loudly about it for over an hour, because Weir was unwilling, as Beckett was, to remove the fetus with no idea how it would affect Sheppard.

However, she couldn't ignore Beckett's warnings, both as a doctor and as... more... he knew Sheppard better perhaps than anyone on Atlantis and if he was correct then they could face a lot of problems down the line.

"Carson, are you sure that what you saw wasn't just John trying to sooth his own discomfort?" Weir asked.

"I wish it was, but he was talkin' to the babe, an' he wasn't just saying things like settle down, he was talkin' to it like it was there and gonna answer him back." Beckett explained.

"Well I don't know what we can really do, perhaps if he'd see Doctor Heightmeyer?" Weir suggested.

"Not in this life time." Beckett said, shaking his head.

Weir frowned, she could order him she supposed, but she didn't feel it would go down well.

"Lets just keep an eye on him, see what happens." She eventually said, hoping that would be enough.

~~~~~

Day 50: Night: Sheppard's Quarters

Sheppard lay on his bed, he was tossing and turning, unable to settle, he couldn't believe what he'd heard, how dare Beckett go to Weir behind his back! He was caught up between being angry or being hurt, with a healthy dose of plain old fear mixed in.

He knew Beckett wasn't entirely wrong, but it was hardly the news of the century, of course he was forming an attachment with the baby, it was growing inside him, how he could be expected not to form an attachment, he didn't know. 

It didn't mean he was losing his perspective, he knew it was a Wraith, he knew it was dangerous, but he couldn't help thinking about Ellia. Before the retrovirus had screwed her up she'd been a good kid, more or less, and Beckett had told him that they were making great progress with the retrovirus now, by the time this kid was born... or even if not then, sometime later, Ellia had eaten normal food when she was younger... there were options.

It wasn't that he wanted to keep the baby. He wasn't the paternal type and he sure as hell didn't have time for it, but what were they seriously thinking of doing? They couldn't kill a helpless baby, they just couldn't. Why was it so bad that he was thinking maybe they could save this baby? That it could live a normal life.

Sheppard was distracted from his thoughts when Beckett came in carrying a tray.

"Dinner time." Beckett said.

"I've already eaten." Sheppard told him, looking sullen.

Beckett frowned, but nodded. "Alright then, well it's just sandwiches and fruit anyway, if you're peckish later."

"I won't be. How's Elizabeth?" Sheppard asked.

"I... she's fine," Beckett answered slowly.

"Yeah, she sounded fine, little tired, maybe she should have my appointment with Heightmeyer, she probably can't sleep because of stress." Sheppard's voice was accusing.

"John, I just..." 

"Went to Weir behind my back, told her I was losing it because I happen to give a fuck about the... I'm not stupid, Carson, I know how dangerous the Wraith are, but this is just a kid! I..." Sheppard paused; he didn't know what he was going to say until he said it. "Get out!"

~~~~~

Day 51: Morning: Infirmary

Beckett woke blurry eyed, quickly realizing he'd fallen asleep in his office. He hadn't meant to, but he'd come here looking to bury himself in work. Anything to stop himself thinking about Sheppard. He hadn't tried arguing with Sheppard when he'd told him to get out, he knew it wouldn't help, the other man was angry and hurt, any attempt to push the issue would only have made him angrier.

"Doctor Beckett..." the quiet voice startled him.

"Radek, what can I do for you?" Beckett asked, trying to look alert.

"I have headache. I do not feel comfortable with Doctor Jericov." The Czech explained.

"Come in, I'll get you something for it." Beckett said, standing, but a wave of dizziness forced him to clutch the desk in support.

"Carson, sit, sit, you are not well." Zelenka rushed to his side, forcing him back into his seat.

"Just a dizzy spell, I'm fine, Radek, really," Beckett protested as the Czech put a hand to his head, as if he were checking for a fever.

"You are very warm. Maybe you are coming down with something." Radek suggested.

Beckett shook his head. "I'm just a wee bit tired, but thank you for your concern it's... thank you."

"I do not think it is just being tired. I think..." Zelenka paused, his head cocking slightly to one side. "You have sore heart."

Beckett might have smiled at the way Zelenka had phrased his words at any other time. The other man he was sure could speak better English than any American and most English men, but he spoke a strange mix of broken English that was quite amusing at times. However, broken English or not, Zelenka had hit the nail on the head.

"Aye, maybe." Beckett conceded, his chest constricting, there was no maybe about it. Sheppard had been livid; his eyes had held an edge of coldness, of hardness, that Beckett had never seen in them before. It had scared him, but more than that it had caused him more pain than he'd ever imagined feeling.

"I will see Doctor Jericov. You will go and rest." Zelenka told him insistently.

Beckett tried to argue. "Radek, I appreciate..."

"You will rest, or I will get Doctor Weir and Doctor McKay." Zelenka said, in what Beckett was sure was an unfair move. He couldn't win, he was sure, so he gave up and, trying to convey an air of normality, he followed Zelenka out of his office, keeping right on going until he entered his own quarters.

A glance around the room assured him he could not maintain control of his emotions, everywhere there were reminders of Sheppard. Beckett sat down heavily on the bed, letting the tears fall.

~~~~~

Day 51: Morning: Sheppard's Quarters

The irritating bleep of his watch forced Sheppard to wake up, but a mixture of the heavy feeling in his abdomen and his heart, kept him stationary on the bed. Sunlight was filtering through the tempered glass and he could smell the fresh sea air, even with the balcony doors closed. He had woken up a million times to similar surroundings, but this time there was a vital component missing. Carson Beckett.

Sheppard knew as soon as Beckett left he had been too harsh, too angry and emotional. Hormones, he had decided, were more evil than the Wraith, at least the Wraith had purpose and some level of predictability. At least he'd always thought so, but given his current state, maybe not.

A sharp kick to his insides confirmed that baby was also awake and further more, that she wasn't amused. Sheppard let out a harsh laugh. He was already thinking of the baby as a 'she', surely Beckett and Weir would have a field day with that little tit-bit. They could share it with Heightmeyer, who would probably want to commit him.

Sheppard didn't even realize he was crying until the baby started to protest more vigorously, the shuffling and shifting only seemed to make it harder for him to calm down as he shuddered through the gasping sobs that sounded far away to his own ears.

He could feel the baby’s distress, sense how agitated she was becoming. "Hush... it's okay." He told her, trying to sooth her, rubbing the bulge in his abdomen where she rested, but it was pointless, he couldn't calm himself, much less the baby.

The harder he tried to calm himself and the baby the less in control he felt, the chaos inside him rushing, confusion and pain that ripped a scream from him for the interminable moment before darkness was the only thing he knew.

~~~~~

Day 53: Evening: Infirmary

Tap, tap, tap. 

It was the only sound in the small back room of the infirmary other than the gentle beeping of the heart monitors. Occasionally, as Rodney McKay looked up from his laptop, sparing a glance for the unconscious man before him, the tapping ceased, only to start again moments later when he returned his attention to his work.

McKay was the only person, other than Doctor Jericov and the nurses - and one fleeting visit from Weir, but she at least had good reason, because she was involved in negotiations with some of their trading partners - that had been there in the two days since Sheppard had been brought in. Personally, McKay could understand that, people were walking on eggshells around the infirmary. Since the moment Carson Beckett had told Jericov to take care of Sheppard, everyone was confused and on edge.

The world, McKay had decided had surely gone crazy. Certainly, he agreed with Weir's assessment that Sheppard was mentally unstable... okay she'd used the word 'confused', but McKay deemed that unsuitable, if he was connecting with a Wraith baby, clearly mentally unstable was the most polite - while still being correct - way to phrase it. But even in that agreement, he didn't understand why Beckett would refuse to treat Sheppard.

Okay technicality, it wasn't a refusal. But he did palm it of on someone else and given that Beckett had once tried to save a very adult, very alive, very ready to eat them Wraith, he failed to see what Sheppard could possibly have done to make Beckett unwilling... fine... reluctant, to treat the man. Sure, Sheppard was occasionally a pain in the ass, but at least he hadn't tried to drain the life out of any of them.

McKay turned away from his work towards the door when he heard it open. "Rodney... sorry I didn't... excuse me." 

"Carson. You are allowed to be in here you know. Practicing your voodoo," McKay suggested trying to make a joke of it.

"No. I just wanted to see that he was okay. I'm very busy. Excuse me." Beckett said hurriedly leaving.

"Whatever you did to him you better be able to undo. Don't take this show of caring to mean anything special, I'm only here because no one else is. But if you don't fix things with Carson and unbreak his heart, I'm going to do you serious damage." McKay announced to the sleeping Sheppard.

See this is why he'd always found it easier not to have friends, there were inevitably emotional issues that just made him uncomfortable. Like whose side he was suppose to choose. Except of course both Beckett and Sheppard were stubborn and nice and would insist he take the other person's side, like that wasn't a complete copout! But he reasoned that he'd known Beckett longer and really it was always best to keep the man with the nice drugs on your side for those inevitable occasions when he ended up in extreme pain.

Of course when Sheppard finally woke up, chances were his eyes would be dark and wounded looking and any ideas McKay had about which side to take would go right out the window, because when it came right down to it both men were his friends and he cared about them too much to abandon either one in a crisis. Next time he decided. Next time two of his friends started dating, he was getting out while the going was good.

~~~~~

Day 54: Afternoon: Infirmary

Bleach, coffee and chamomile teased his nose, telling Sheppard that he was in the infirmary and exactly who was with him before he ever opened his eyes.

"Welcome back to the land of the living. Dr Jericov is coming now." McKay's voice cut through the haze in his mind, confirming his nose had been telling the truth, but Sheppard was not pleased to hear Jericov's name. Where was Beckett? Was he hurt?

"He's in his office having tea last time I checked actually. Whatever you did to screw things up had better be fixable, or I'm going to be very cranky with you for a long time." McKay informed him, but his voice held no edge of anger and his eyes when Sheppard looked at them were tinged with sympathy. Well he supposed that answered that then, Beckett was clearly avoiding him like the plague, because the man had been more willing in the past to treat a Wraith than he was to treat his own lover now. Sheppard frowned as his mind unhelpfully supplied 'ex-lover'.

"Ah, Colonel Sheppard. Good, good, you are awake. We were most perplexed by you, most perplexed, but we think you will be fine so long as you rest plenty and do not stress yourself." Jericov told him, his Russian accent tinting his speech, despite the fact, as Sheppard understood it; the man hadn't been to Russia since he was six.

Sheppard didn't bother responding however, though internally he was ready to fall off the bed laughing to himself. He was the first pregnant male in human history, pregnant, further more, with a Wraith, who clearly had some sort of mental connection going on, that might or might not be controlling him and, oh yes, his lover... ex-lover, hated him so much he couldn't even cover it with a mask of professionalism long enough to treat him! Surely that situation was not conducive to 'not stressing himself'.

Not that Sheppard was feeling sorry for himself, no, because he was a Sheppard, son of David Sheppard, who had been top notch brass and who would roll in his very proper military grave if he thought his son was feeling sorry for himself. Of course, he'd probably rolled himself into a stupor long before now at the notion his son was regularly taking it up the ass from a *civilian* doctor. Yup, Sheppard was certain his father would be totally ashamed of him, even more so if the old bastard thought for one second that his son was seriously thinking of jumping of the nearest balcony because at least then it would all be over.

~~~~~

Day 54: Evening: Beckett's Quarters

Beckett felt restricted, like he was locked in, even though logically he knew he could leave at anytime, it just didn't feel like that. Even though they had spent most of their time together in Sheppard's quarters, there were just enough reminders of Sheppard in his own room to make it impossible to try and forget him.

He had heard from Jericov that Sheppard was awake and had been returned to his quarters under strict orders of rest. The Russian had looked at him with pity as he told him Sheppard's condition and Beckett had been torn between relief and the urge to punch Jericov, because really, what right did the man have to look so... sympathetic!

Weir had come by to see him under the pretence of work and he'd seen her cast worried glances towards the back room, he felt guilty that he was pleased at Sheppard's lack of visitors the last few days. Of course it wasn't, he knew, that people were avoiding visiting Sheppard; they were just avoiding doing it when Beckett was around. All except McKay, who glared at anyone who shot him disapproving looks, daring them to make something off it.

It made Beckett both glad and self-conscious, people were so clearly taking his feelings into account when it came to Sheppard, but at the same time, Beckett wondered how many people, other than McKay, were taking Sheppard's feelings into account. Weir, he was sure was, but she had been very busy and even so she'd go out of her way not to offend or hurt either of them, but so far everyone else seemed to be showing far more concern for him than for Sheppard.

McKay had scoffed at him earlier, telling him to get over himself, because really, people just didn't want him to break down and cry, where as clearly, Sheppard being unconscious couldn't get hurt by what anyone else was saying or doing and they didn't run the risk of making him cry. Although, McKay had also agreed that Sheppard probably wouldn't cry even if he was awake. Military mindset and all that.

Beckett felt honestly tired. He wasn't even sure he could be angry anymore, he just felt drained and empty. Like his insides had slowly dribbled out through his tear ducts and there was nothing left.

~~~~~

Day 56: Morning: Sheppard's Quarters

"Just so I know, how long are you planning on this self-imposed exile? Because self-pity, I have to say, isn't a good look on you. And if we're expected to still feed you for the foreseeable future, I'm going to have to set up some sort of rota system, because I am far too important to be wasting valuable time on being a waiter. I have a back log of work that would take my entire life-time even if nothing new was ever added to it." McKay primly informed Sheppard. He wasn't being mean or rude, he was just being McKay and really not all that wrong, because there were just too many important things he had to be doing, that were more valuable to the human race than making sure John Sheppard got enough Vitamin C.

"I never asked you to bring me food." Sheppard said, his voice dull, even. McKay hated that voice, it completely lacked the spark that had made Sheppard so... so worthy of being his best friend.

Yes, McKay had finally decided that while he loved Beckett (in a completely non-sexual because seriously ewww, way), Sheppard was the best friend he'd ever had. They understood each other and that was pretty damn special (in, McKay reminded himself, a completely non-sexual way, because Sheppard might be smart, but he wasn't blonde and he completely lacked one vital component to McKay's idea of a perfect mate, mainly that he didn't have breasts).

"No of course you didn't, but Elizabeth would be truly pissed off at me if I let you die of starvation." McKay told him.

"Elizabeth worries too much. I'm fine." Sheppard said, eyes a dull green that refused to meet McKay's own.

"Of course you're fine. You barely eat, barely sleep, don't say more than a few lackluster words per day. If you were anymore giddy and fine we'd be forced to sedate you. You know Heightmeyer is practically foaming at the mouth trying to get her claws into you? I'm sure she reckons she can make her fortune from you, or at least win some auspicious prize for curing what ails you." McKay idly opened a power bar while he was talking.

"I don't need Heightmeyer." Sheppard growled, in what was probably the most emotional reaction McKay had seen in days.

"Of course you don't, you have me and if anyone is getting any auspicious prizes I think it should be me. I mean who else would bring you freeze dried chicken noodle soup when they could be off discovering the secrets of the ancients?" McKay told him matter of factly.

"I'll be sure to nominate you for something auspicious," Sheppard said, a hint of the old John Sheppard showing through in his sarcasm.

"Well, you know, I'd have a greater chance of getting that prize if you actually you know... spoke to me." McKay said, in a falsely casual way that not even a blind man could have missed.

"Nothing to speak about." Sheppard told him.

McKay frowned. "I'd beg to differ. You're surly and quiet. Even Kavanagh has commented on it. I mean Kavanagh, man twice voted least likely to notice anything not pertaining to his own untimely demise!"

"He's not that bad," Sheppard said, completely convincing McKay that he wasn't well, because no one would ever aloud admit that Kavanagh was anything but a royal pain in the ass. Even if McKay did quietly agree that no, Kavanagh wasn't that bad.

"John, everyone is concerned. And I know I'm not the best person for this, I'm completely aware that my social skills are on par with a blind, deaf, dumb, blonde poodle, but..." McKay paused. God he really sucked at this! Beckett would know what to say, except apparently he didn't, because Beckett wasn't saying much of anything to anyone that wasn't work related.

"I don't need anyone's concern! I'm fine. F. I. N. E. Fine! Why won't everyone just leave us alone? Carson got the hint, why can't you?" Sheppard yelled at him, jumping up and moving around until his fist connected with McKay's jaw.  
.  
"Fuck!" was the last thing McKay heard before he blacked out.

~~~~~

"Rodney... McKay, come on wake up, don't make me have to call Carson." Sheppard pleaded, relief flooding him when McKay groaned and opened his eyes.

He seemed to be thinking for a moment before he said "Us?" in that way that suggested he wasn't going to go away until you either killed him or answered him. Sheppard sighed.

"I know you're going to say I'm nuts, maybe I am nuts but... I can feel her, Rodney; she's a living thing, right here. She can be happy, or scared, just like we can." Sheppard said, his hand automatically resting on his abdomen. There was no doubt now he was pregnant and he looked it.

"You want to keep it?" McKay asked. It was only half questioning. Sheppard knew for all McKay's social ineptitudes, he could read Sheppard pretty damn well.

"It's crazy I know, but she's just a baby. We already know young Wraith eat normal food and Carson is still working on the retrovirus maybe by the time... she's my baby." Sheppard said, his voice quiet and serious.

McKay, it was clear, did think he was crazy. Or maybe he just had a concussion. He was looking at him with wide eyes and doing a fine impression of a fish and Sheppard laughed internally as he imagined McKay suddenly sprouting gills and diving over his balcony to go live with whatever the ancient version of mermaids were.

Hysteria seemed to set in, because without meaning too Sheppard was laughing out loud, practically rolling on the floor, unable to stop the manic cackling, until McKay helpfully slapped him.

"You know, that wasn't necessary." McKay said, flushed with annoyance and doing his best impression of a pouting child. Or at least what Sheppard thought was probably his best impression; he could picture a younger Rodney McKay giving that look to his parents every time they didn't give him exactly what he wanted.

"Sorry." Sheppard told him, trying to be solemn, but it was like a weight had been lifted off him and he felt calm in a way he hadn't in weeks.

"Hmpf! Does Carson know you want to keep it? Is that why he refuses to go anywhere near you?" McKay asked.

"No. Maybe. I told him to go, he... I heard him talking to Elizabeth about me and I guess I overreacted. It doesn't matter anyway; he wouldn't want this baby anymore than any other sane person would." Sheppard said.

McKay snorted. "Well, you want it. Of course, sane is perhaps not a word I'd associate with you. You know you'll have to discuss it with him eventually, he is chief medical officer if nothing else, not to mention Elizabeth is going to have a heart attack."

"I know. Would you keep it?" Sheppard asked.

McKay actually seemed to think about it. Sheppard had to wonder what was going through his mind and after a few moments he got his answer.

"No. Not just because it's Wraith either, but because I'm me. I'm not the paternal type, I don't get along with children. I had a project in school once where we were paired of and had to look after a fake baby for a week. I got stuck with Mary Kisnor as my partner, mainly because no one else would have me. I was two years younger than everyone else in my grade and even then the work was too easy. First day I left it in the library for six hours because I forgot it. Second day I forgot to give it breakfast and lunch. By day four Mary refused to even let me *look* at it. Probably for the best, except she let it drown in the bathtub. She has five kids now though, all of them screaming little menaces." McKay rambled, but it was an honest answer. Not that McKay was ever anything but, the scientist had a low tolerance for bullshit, which sometimes was a curse when dealing with new people, but Sheppard himself found it refreshing for the most part.

"I got an A+ for our baby assignment. Of course we had an odd number of boys to girls in our class, so I ended up with a husband instead of a wife. I wonder if Ms. Chaney knew I was gay?" Sheppard smiled at that idea. Ms. Chaney had been a upstanding lady in the community and heaven help anyone who said a word against her or her partner in crime, Miss. Evans, who ran the local day care centre.

"I very much doubt that. Of course, if you were always such a pretty boy, it's very possible." McKay smirked at him.

"If I did this, they'd send me back to Earth wouldn't they? Assuming Carson's retrovirus worked." Sheppard said.

McKay nodded, a little frown on his face. Sheppard closed his eyes leaning back against the bed, realizing for the first time that they were still on the floor. Oh well he was comfortable and there was no way he was getting up without help, besides it was kinda nice down on the floor, Ancient floor tiles were heated.

"I'll talk to Elizabeth." Sheppard promised, letting himself fall into a light sleep until McKay forced him up and into bed. By the time he woke again it was already dark outside.

"I'll talk to her tomorrow." He told himself, rolling over to find a tray with sandwiches and a flask of coffee that was still warm, a note scrawled in McKay's distinctive handwriting telling him Weir would be bringing him his breakfast in the morning, so there was no getting out of talking to her.

~~~~~

Day 57: Morning: Sheppard's Quarters

Weir knocked lightly on the door, waiting for admittance, which came faster than she was expecting. Sheppard was sitting up in bed, War and Peace on his knees and what looked like liquorish sticking out of his mouth.

"Novak brought it. Apparently her sister swore by it for morning sickness. Hasn't stopped me being sick, but it does taste good." Sheppard told her, holding out some in offering.

"No thank you. I brought you breakfast. Rodney said you liked the pancakes with..." Weir made a face "...marmite."

"Oh yeah!" Sheppard's face light up, as he immediately started digging into the offering as soon as the tray was set on his knees.

"I want to keep the baby." He said around mouthfuls, making it sound more like 'ibaunttokipehbebe' but Weir got the general gist. She'd been afraid of this. Of course she couldn't outright order him not to. But she didn't want to lose her military commander, even if she was ready to believe this child wasn't a danger, and she wasn't there yet.

Still, she nodded, kept her most diplomatic face firmly in place and said she'd discuss the viability of using the retrovirus with Beckett. She wondered what kind of person it made her that she hoped Beckett would say it wasn't ready and he wasn't ready to test it on a baby.

~~~~~

Day 57: Afternoon: Infirmary

"Absolutely not! Even if I thought it was ready for testing I wouldn't test it on a baby. No!" Beckett said, quite irritated that Weir would even ask him such a thing. To test an unproved treatment, one that had already failed in the past, on a baby. It was... inconceivable.

"I had to ask, Carson, though I must admit I'm relieved by your answer. However, Colonel Sheppard does want to keep this child and I don't think we'll have a great deal of success in trying to talk him out if it." Weir said.

Beckett wanted to shout, or throw something, or maybe hit someone. If he'd been a more violent man he might well have done so, but instead he settled for collapsing into his chair with a loud sigh. What was Sheppard thinking? It was ludicrous; they were talking about a Wraith, at the very least, part Wraith.

Beckett was entirely ready to tell Weir exactly what he was thinking when a loud crash drew their attention to the main infirmary where McKay was attempting to hoist Sheppard onto a bed and only half succeeding. Sheppard it seemed wasn't being very helpful, mostly Beckett suspected because he was in a great deal of pain.

"Rodney?" Weir asked as they approached.

"He just collapsed in pain." McKay said breathlessly. Beckett looked around but he knew it was pointless, Jericov was on the mainland and Sheppard needed help now, whatever his personal feelings were, Beckett shoved them as far back in his mind as he could and turned to Sheppard, who was finally sitting properly on the bed.

"Where is the pain, Colonel?" he asked.

Sheppard grabbed his hand and placed it over where the baby was, his mouth open in a grimace, teeth clenched tightly, clearly trying to hold back from screaming out loud.

Beckett did the only thing he could and gave Sheppard the highest dose of morphine he could safely give him, relieved when he finally relaxed into a drug induced sleep.

~~~~~

Day 65: Night: Infirmary

Sheppard felt weightless, like he was floating somewhere above the rest of the universe looking down. He couldn't seem to remember who he was, or where he was, only that there were voices. Different voices, ones he didn't know, talking softly, whispering reassurances, but he didn't know why, or who, only that he liked the soothing feeling that washed over him when he felt gentle fingers tickling at his scalp.

"He's starting to come around, he has odd flashes of consciousness, but it'll be another day or two before he's properly lucid. If we'd waited even an hour more he wouldn't have survived." The soft lilt made Sheppard smile, he knew that voice. That voice loved him.

"Is there any change in the baby’s condition?" Another voice, female, a friend, he cared about her.

"Nothing. She was born too soon. But even if she hadn't been, the Wraith didn't do a very good job. She's half human alright and normally I'd say that wasn't a problem, but they clearly used two sets of male DNA to create the child and their processes were flawed. I'm not convinced the Retrovirus would save her now even if I was willing to try it." That lilt sounded sad now, Sheppard wondered what they were talking about, he felt like he should know, but the harder he tried to figure out what was going on, the further away the information seemed to get. Eventually he fell asleep again.

~~~~~

Day 67: Afternoon: Infirmary

"John, do you know where you are?" Weir asked softly, a hand resting on his arm. A gesture of comfort, he recognized, moments before he realized he could no longer feel the baby inside him.

"Atlantis. Is she dead?" he asked, his eyes glistening and his voice scratchy from disuse.

"No. She's very ill." Weir admitted, dropping a few ice chips into his mouth.

Sheppard swallowed the chips, coughing. "The retrovirus..." Sheppard murmured, but he sunk back to sleep before he could hear the answer.

~~~~~

Day 68: Night: Infirmary

Sheppard finally felt awake, instead of the half wakefulness he'd occasionally been feeling the last few days. But it was dark and the infirmary quiet, he wanted to call for someone, but he didn't know who to call. He strained to get up, but every move sent pain lancing through his abdomen.

"Dr. Beckett won't thank you if you break his stitches." The voice from the side startled him.

"Kavanagh?" Sheppard asked, trying to see in the dim light.

"Well unless I turned into someone else when I wasn't looking." The scientist said.

"Oh. Is... I mean..." Sheppard wasn't sure what he meant.

"She's in an incubator. Beckett had one scrounged up when they discovered you were pregnant. He brings her in here sometimes, but you've been asleep." Kavanagh told him.

"I... why are you...?" Sheppard made a hand signal that should have meant 'in here' but in the dark it didn't much matter what it meant because Kavanagh couldn't see it.

"Slight accident in one of the labs a few days ago." Kavanagh told him.

"Slight and you've been in here for days?" Sheppard asked.

"Not everyone is a hypochondriac like McKay. Besides, it was slight in the sense that only I got hurt. Major would be if every bed in here was taken up by scientists." Kavanagh said, sounding nasal and smarmy but Sheppard had to admit Kavanagh had a point about McKay and his hypochondria.

"No. I guess not." Sheppard agreed. He didn't have much else to say and he doubted Kavanagh wanted to talk to him, even if he had anything interesting to say. He wanted to see his daughter... "It was a girl!" Sheppard said suddenly and louder than he'd meant to.

"Yes, it was." Kavanagh agreed. "This is why I said 'she'."

"Oh, yeah. Sorry I just... I thought so but I didn't..." Sheppard went quiet again.

"She has you're eyes according to Beckett. Definitely has your hair, dark and messy." Kavanagh said. Sheppard turned towards the voice. He couldn't see more than the vague outline of the scientist, but he listened while Kavanagh told him everything he knew about what had happened since Sheppard had been brought into the infirmary, until he fell asleep as the sun came up.

~~~~~

Day 69: Morning: Infirmary

"I can't take her out, I'm sorry." Beckett said, pulling the incubator along side Sheppard's bed.

He'd spent a lot of hours over the last ten days looking at the baby, but this was Sheppard's first look. Beckett tried to shake off the internal voice that told him it might be his only look. There was nothing they could do for the baby now, she was too far gone. Even if he was willing to administer the retrovirus, which he wasn't, he didn't think it would matter.

Sheppard looked a mixture of happy and sad, two emotions that shouldn't go well together, but there it was, plain as day on his face, awe in his expression and tears in his eyes.

The little girl that Beckett had delivered by C-Section looked almost entirely human. She had green eyes and short tufts of dark hair, which stuck up at odd angles; only the two small scars on either side of her nose separated her from a healthy human baby. Beckett wondered if she would have grown to look more like a Wraith as she got older, but he knew he'd never find out.

"Carson, there has to be something, anything that..." Sheppard begged, tears rolling down his cheeks.

"I'm sorry. I can't give her the retrovirus; it isn't safe after what happened to Ellia, even if I could I don't believe it would make any difference." Beckett said softly.

"Can't or won't?" Sheppard asked, his voice accusing.

Beckett wondered himself, if he was just using Ellia as an excuse to rid himself of the thing that had torn him and Sheppard apart. "I'm sorry." Was all he could say however, because he wasn't sure he'd ever know for certain, if his reluctance was personal or professional.

~~~~~

Day 70: Evening: Infirmary

Sheppard hadn't said a word since McKay had entered the infirmary. In fact, he understood that Sheppard hadn't uttered a word all day. Dex had called him 'haunted'. McKay couldn't disagree.

Finally, McKay had no choice but to retreat, because it seemed clear that Sheppard wasn't going to speak and it seemed rude to do work on his laptop, as he had before when Sheppard had been less than talkative. Of course on those occasions, Sheppard had been unconscious, now he was awake, so it seemed rude to work on power regulation when Sheppard was conscious two feet away.

He murmured a good night, even clasping Sheppard's hand in what was the most comforting way he could manage, but there wasn't even a flicker of recognition from Sheppard. Perhaps, McKay decided, haunted wasn't the proper term. Sheppard looked like he should be the one doing the haunting, he looked dead inside.

~~~~~

Finally he was alone. All day, everyone, it seemed, had come to see him. Weir, Teyla and Dex, Zelenka, Bates, even Caldwell had stopped by. Didn't they know he didn't want to talk to them!

He wasn't angry, or even sad. Honestly Sheppard wasn't sure there was a word for what he was feeling, but the closest he could think of was guilty. He wasn't sure why really, it was hardly his fault the Wraith had fucked things up when they dropped a baby inside him and expected him to play Colonel Mom, but he felt guilty anyway.

Guilt, he knew he could handle, but it was more than simple guilt, it was something else, something he couldn't name something that didn't make sense. Whatever it was had settled itself in his heart when he watched the heart monitor Beckett had attached to his daughter’s chest flat line. There had been no sounds, no theatrics, no last ditch attempts to save her. The squiggly line had just flattened out and then it was over.

He felt like she should be angry. Like he should scream and holler and make people understand, but he couldn't find the energy to do it, he couldn't find the emotions he needed, they just weren't there.

Twelve days, fifteen hours, forty-seven minutes. That was how long his daughter had lived. It felt wrong, because he hadn't been aware most of that time, he hadn't been by her side, he should have been, but instead she'd been alone. Using more energy than he thought he really had, Sheppard forced himself out of bed, being as quiet as he could, he let Atlantis guide him.

~~~~~

Day 71: Dawn: Atlantis: Balcony

The chill of the night was starting to fade, but the sun wasn't yet up and it wasn't quite as warm as it could be. On a balcony on Atlantis' east pier there were two lifesigns.

"People are looking for you."

Sheppard was startled, he hadn't heard anyone approach. "I'm not exactly hard to find. You found me." He answered tiredly.

"I was intelligent enough not to trust the Ancient sensors. Atlantis likes you, she's hiding you." Kavanagh said. Sheppard snorted, he wondered how much McKay would kill Kavanagh for figuring that out before him.

"Then how did you know I was here?" Sheppard asked.

"Furthest secure balcony from the tower. At least, within a reasonable distance from a transporter. I didn't think you'd be able to walk far." Kavanagh replied, pulling his jacket around him.

"Since when are you a tactician and a medic?" Sheppard asked caustically.

"I never was either. Never would be, guns and blood, not on my top ten list of things to have regular contact with." Kavanagh said.

"Why are you here? Why didn't you tell someone else you're great idea?" Sheppard asked.

"Because, even if I did they wouldn't listen. Besides they'll all just molly coddle you and I don't think you'd like that." Kavanagh surprised Sheppard with that insight, it was true, he didn't want to be coddled, just left alone. Of course it didn't seem likely that Kavanagh was planning on leaving him alone.

"She was alone. She only lived for 12 days and she spent almost all of them alone. I promised myself she'd never be alone like I was." Sheppard said, surprising both himself and, it seemed, Kavanagh with his statement.

"Possibly you weren't listening that night in the infirmary, but Beckett barely left her side, or yours the whole time you were out. Just dumb luck and a nice tranquilizer from Jericov that got him to bed that night." Kavanagh said, his voice entirely unsympathetic, even scolding. Sheppard imagined he was thinking something like 'stupid air force colonel's don't listen to what they are told'. Of course, he apparently hadn't listened to what he was told, so Kavanagh wouldn't have been wrong in thinking that.

"Are you planning on freezing to death out here? Or maybe jumping off, because if you're going to do either, can you do it quickly, I'm cold and I'd like to go inside." Kavanagh added a few moments later.

Sheppard looked up at him. He wasn't attractive, his voice was irritating after a while and he tended to piss off just about anyone who was in the room with him for more than thirty seconds at a time, but Sheppard decided he liked him.

"I'm just going to stay here a while longer. But... you better tell Dr. Weir where I am, I don't want you to get into trouble." Sheppard told him.

"I'm perfectly capable of getting myself out of trouble again, Colonel. I'll tell them in an hour or so, that enough time?" Kavanagh asked.

Sheppard nodded and actually felt himself smile a little, because Kavanagh was possible the most hated man on Atlantis, second only to Kolya, and Sheppard found he really didn't hate him, that maybe the man wasn't as much of a bastard as McKay claimed, that maybe even he was pretty okay, in a geeky sorta way and that was nice.

"Don't go getting excited, Colonel, I'm every bit the bastard McKay would have you believe, but that doesn't mean I'm completely incapable of feelings." Kavanagh said, like maybe he'd read Sheppard's mind, or maybe Sheppard had spoken out loud, he wasn't sure which, but before he could ask he was left alone again.

He wanted to bury his daughter... Alicia, on the mainland. And he needed to talk to Beckett. Maybe to fix things, maybe just to help fix himself. And as the sky turned from dark blue to a brilliant mix of purples and reds and dazzling oranges, Sheppard fell asleep, watching the waves from where he sat on the balcony.

When he woke up, he was still there, the sun high in the sky and a soft voice murmuring in his ear, he wasn't alone.

**Author's Note:**

> *spoilers*  
> *spoilers*  
> *spoilers*  
> *spoilers*  
> This story contains non-consensual mpreg (not rape however) and the death of a young baby. If this is likely to upset you, please use some caution.  
> *spoilers*  
> *spoilers*  
> *spoilers*  
> *spoilers*


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